Tuesday, July 9, 2013

Here’s a New Paper on a Long Non Coding RNA

Wow

Genes in our DNA code for proteins, but those genes only account for a few percent of the entire genome. What is the rest of our DNA doing? Evolutionists thought it was mostly useless but, in fact, all kinds of functions have been implicated. Some of the DNA is transcribed in long segments but, unlike the coding genes, does not get translated into a protein. Instead, this large noncoding RNA (lncRNA) helps to regulate which protein-coding genes are transcribed. New research is helping to elucidate how lncRNA does its job. The findings are not only astonishing, they demolish evolutionary theory.

The new research studied a particular lncRNA, known as Xist, that directs X-chromosome inactivation. The researchers found that Xist performs a three-dimensional, spatial, search for key protein-coding genes and directs the rearrangement of the chromosome. The key genes, though far apart along the chromosome, are close together in the tangled chromosome structure and can be regulated as a single group by Xist. As one researcher explained:

You can now think about these lncRNAs as a way to bring together genes that are needed for common function into a single physical region and then regulate them as a set, rather than individually. They are not just scaffolds of proteins but actual organizers of genes.

So not only is the lncRNA DNA sequence important to perform its job, but its location and the locations of the other genes are important. And all of this depends on the intricate, three-dimensional structural details of the chromosome. As the researcher further explained:

LncRNAs, unlike proteins, really can use their genomic information—their context, their location—to act, to bring together targets. That makes them quite unique.

Indeed. Not only would random, chance mutations need somehow to luckily hit upon the lncRNA DNA sequence, but they would have to do that in the right place in the genome. And the chromosome structure, and location of the key genes and their packing proteins, need to support this incredible capability. Here is how one writer explained the findings:

Before Xist is activated, X-chromosome genes are all spread out. But, the researchers found, once Xist is turned on, it quickly pulls in genes, forming a cloud. “And it’s not just that the expression levels of Xist get higher and higher,” Guttman says. “It’s that Xist brings in all of these related genes into a physical nuclear structure. All of these genes then occupy a single territory.”

Evolution

The lncRNA’s function reveals that evolution is even more unlikely. Evolution is a theory of a large number of low probability events. Evolving the sequence is itself unlikely (evolutionists say it arose from mutations combining portions of a dead protein gene and mobile elements). Now those random mutations must do the job in the right place, within the genome, as well.

But that is not all. For lncRNAs such as Xist are not even well conserved across different species (it is not found outside the eutherians), as evolution predicts and expects. Such lack of sequence conservation, evolution predicts, should mean lack of function. But lncRNAs such as Xist obviously do not lack function.

This leaves evolutionists with nothing but yet another just-so story as their only alternative; namely, that lncRNAs such as Xist underwent “rapid evolution.”

Evolution predicts certain patterns to be found amongst the species, and when they find those patterns evolutionists proclaim them as proof of evolution. But when unique designs are found which contradict evolution’s expectations, which is far more prevalent than the textbooks reveal, evolutionists quietly explain them away as the results of “rapid evolution.” Here is how one paper explained the evolution of Xist:

The mammalian transcriptome contains many non-protein-coding RNAs (ncRNAs), but most of these are of unclear significance and lack strong sequence conservation, prompting suggestions that they might be non-functional. However, certain long functional ncRNAs such as Air and Xist are also poorly conserved. In this article, we systematically analyzed the conservation of several groups of functional ncRNAs, including miRNAs, snoRNAs and longer ncRNAs whose function has been either documented or confidently predicted. As expected, miRNAs and snoRNAs were highly conserved. By contrast, the longer functional non-micro, non-sno ncRNAs were much less conserved with many displaying rapid sequence evolution. Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function.

As highlighted above, this paper explains the lack of conservation, across species, of Xist and other lncRNAs, as a consequence of “rapid sequence evolution.” In fact, the paper goes further, making the non scientific claim that these lncRNAs display rapid sequence evolution.

That is, of course, a misrepresentation of the science. Resorting to an unfalsifiable, unlikely, explanation is one thing. It is even worse to present that explanation as a given. LncRNAs do not display rapid sequence evolution any more than a football field displays a flat Earth.

Ever since Darwin, evolutionists have required long time periods. Darwin was greatly concerned about Lord Kelvin’s arguments that the age of the Earth was limited to 100 million years. And evolutionists celebrated the resolution to those arguments and the upward revision of the Earth’s age into the billions of years. But when deep time is unavailable, such as with the origin of Xist, evolutionists simply enlist “rapid evolution.”

Did Xist evolve? Perhaps, perhaps not. Who knows what future research will reveal. But from a scientific perspective, the current evidence is abundantly clear. It is astronomically unlikely that Xist, with its amazing capabilities, evolved. The fact that it must have evolved “rapidly” adds an exclamation mark to the finding. An intricate sequence must have evolved with amazing functionality. Those random mutations must have evolved Xist in the right place within the genome. And all this must have happened rapidly, at the right time. The right sequence, the right place, and the right time. When it comes to science, evolutionary theory simply makes no sense.

25 comments:

I never cease to be impressed by the wonders at work within living things.

The abstract in this paper suggests Xist evolved (at least partly) from another protein coding gene.http://www.sciencemag.org/content/312/5780/1653

I would be interested in how much "partly" means and also interesting that they note that the mechanisms of dosage compensation have evolved independently at least twice - something that seems to happen a lot.

Nonetheless, as they report: "We show here that Xist evolved, at least partly, from a protein-coding gene ...". This non scientific certainty comes right out of the metaphysics.

This later paper diplomatically corrects them ("Previously it was proposed ..."). That paper says Xist "emerged de novo in early eutherians (from a combination of exons and mobile elements)". One way or another, they need an unlikely sequence to arise rapidly at the right place.

Thanks for the link, just goes to show does't it. Makes it harder to fully commit to studies like this when despite "we show here that Xist evolved" which sounds pretty conclusive... later turns into "emerged de novo". Really does not help the cause.

Well I do appreciate the more scientific tone of the Elisaphenko paper. Nonetheless, it simply assumes evolution, regardless of how unlikely:

Comparative analysis across different species shows that eutherian Xist evolved in a species-specific manner. As reported previously the unique sequence of the Xist gene is not conserved and evolves very rapidly. The exon-intron structure of Xist is also not strongly conserved. The interspecific differences in the unique sequence, length and structure of exons suggest that the length of the RNA (and, consequently, the sequences, like mobile elements and tandem repeats, contributing to the RNA size in different species) is either non-essential for function (neutral sequences) or these sequences became selectively adapted in a specific manner to the conditions of functioning in the genome and the X chromosome of particular species. Certain core sequences common for all species are essential for the regulation of gene activity and its function. …

Thus, we have proposed a mechanism whereby the Xist gene may have originated. We suggest that the Xist gene lost the function of the protein-coding gene Lnx3 and no longer contained any extended ORFs. However, due to transposon insertions and their partial subsequent amplification, new functional domains formed (for example, repeat A in exon 1 [17]). These domains then became necessary for the transcriptional silencing of X chromosome genes. We suggest that this example of how a protein-coding gene loses its protein-coding function by mutation and then gains a new function due to transposon integration is not an exceptional case, but is a more wide-spread phenomenon applying to other non-coding RNA genes and pseudogenes with new functions.

Of course it assumes evolution, because evolution is a done deal, and has been for a long time. There is no question that life has evolved. Therefore scientists take it for granted and study how evolution has occurred.

Unless of course you're a teacher at a Bible college whose mission it is to brainwash young people into believing creationist bullshit.

Of course it assumes evolution, because evolution is a done deal, and has been for a long time. There is no question that life has evolved. Therefore scientists take it for granted and study how evolution has occurred.

So evolution is a fact huh? And how do evolutionists know that to be true? Oh, because there are fossils revealing different species that came before (even though the species appear abruptly and then die off due to extinction). And there are all kinds of similarities and differences between the species (even though those patterns don't fit evolution's expectations). And we can observe change from both breeders and in the field (even though breeders have long since known their change is limited and the change we observe in the field comes from complex adaptation mechanisms that evolution cannot explain).

You see evolution isn't about science, it is a dogma. And then they blame us for it, even though we're not dogmatic about origins. Funny how that works.

Elijah.Wheres that exact quote(So when you told us you had no opinion on the validity of evolution)

DrHunter,It would be an abuse of science to say the evolution of such systems is a fact, or likely. I don’t care if evolution is true or not,but from a strictly scientific perspective (which is not how the theory is motivated or evaluated), the idea is, to be frank, just silly.

So he has an opinion on the validity,he just doesn't care if he is right or wrong.

Ah Cornelius, you forget that nothing in biology makes sense except in the light of evolution.

On a more serious note thought, a quick delving though papers courtesy of google and google scholar shows that there are a number of questions posed and issues raised around Xist and inavtivations.

Take:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695352/"There is at present no satisfactory explanation for the origin of the X chromosome inactivation. The inactivation mechanism could have emerged de novo on the X chromosome or could have been borrowed from the existing silencing process."

These papers contain a lot of speculation and discovered discrepancies. I wish they would focus more on the function and less on trying to postulate how it evolved.

Yes, that's a good example. The just-add-water narrative always becomes more complicated. For instance, don't forget that the histones and promoters needed to be modified as well:

The evolution of complete and stable inactivation was accompanied by substitution of the noncoding RNA Rsx by Xist and the emergence of Xist -dependent modifications in the histones on the inactive X chromosome, along with DNA methylation in promoters

Also, think of the incredible serendipity that a protein-coding sequence could turn right around and serve as an RNA sequence:

The Lnx3 gene, whose protein product contains the ubiquitin-ligase domain PDZ, underlies the formation of Xist (Fig. 4). It has been shown by comparing these genes that the promoter region and at least three exons of the Xist gene originate from the sequences of the Lnx3 gene.

Kind of like saying an encoded message could also be used as an unencoded message.

More serendipity as parts as disparate as (i) protein-coding exons, (ii) endogenous retroviruses, and (iii) mobile elements of various classes, just happen to work together to construct the incredible Xist gene.

The largest first exon of the Xist gene presumably descended from endogenous retroviruses, whose fragments (after having been inserted into the locus) were amplified, producing simple tandem repeats of several types, which have been identified within it. The remaining exons of the Xist gene are syntenic to mobile elements of various classes.

The findings are not only astonishing, they demolish evolutionary theory.

LOL! There goes poor old evolutionary theory being "demolished" again.

What's that make, about 15,000 times in the last dozen decades Creationists have proclaimed ToE to be finished? Heck CH, you personally have falsified ToE several hundred times all by yourself, right? And still no Nobel Prize....

Thorton (man that is hard to type without thinking of chocolates) as far as a Nobel prize goes I wouldn't get your hopes up - I doubt they would give one for simply disproving a theory, especially one so widely accepted; humans are not well know for swallowing bitter pills with grace you know. Much more likely for producing an alternative theory I should think, but that seems to be an impossible task.

It's actually T. Horton, like the Canadian doughnut chain. Not that it will help with the cravings much :)

as far as a Nobel prize goes I wouldn't get your hopes up - I doubt they would give one for simply disproving a theory, especially one so widely accepted; humans are not well know for swallowing bitter pills with grace you know.

Au contraire. Anyone who manages to disprove ToE would go down in history as one of the most famous scientists of all times.

Much more likely for producing an alternative theory I should think, but that seems to be an impossible task.

It's certainly proven impossible for the Creationists and IDiots so far.

Thanks. Someone should make a catalog of divine creation in history. It would be an interesting read. Perhaps it could be a collaboration between a theologian and a biologist, sort of the when and why.

The timing of this creation is interesting. It was after the first life, and well before the human (in God's image) soul. Since it goes so far back there is almost no time to evolve. Evolution's deep time argument is meaningless. That really shows how impossible it would be for Xist to evolve. It is a good context within which to expose the contradiction of 'rapid evolution.'

The timing of this creation is interesting. It was after the first life, and well before the human (in God's image) soul. Since it goes so far back there is almost no time to evolve. Evolution's deep time argument is meaningless. That really shows how impossible it would be for Xist to evolve.

How so? Life on the planet dates back well over 3 billion years before the evolution of the mammals. Multicellular life dates back to roughly 500 million years before mammals. Why is that "almost no time" to evolve?

And you bible thumping creationists are not dogmatic about origins, right? Pardon me while I LMAO."

What if they were dogmatic? So what?

What if there were not "bible thumping creationists" around that allows you to create this, staw man, false dichotemy that you love to promote in order to make it appear that "science" supports the NDE conjectures with "real evidence"?

Anybody looking in, LOOK AT THIS OBSERVATION. This is all there is to that argument. Nothing more.

No one can demostrate that NDE processes can create a single protein, let alone, even a relatively "simple" complex of proteins such as a bacterial flagellum.

But, why let details stand in the way of a beloved philosophical position of a staunch, anti-realist intent on promoting an opinion.

I, for one, am waiting for REAL EVIDENCE, for and NDE position. "I hope you will join me, and the world can be as one."

(taken from another ignorant philosopher, who made it big in the electro-magnifier socio-promulating machine. That says, "if it can be put out to millions, it becomes truth".

You know Dr. Hunter,The NLT James,1:18 He chose to give birth to us by giving us his true word. And we, out of all creation, became his prized possession.

When you reveal the intricacies of the DNA and how it works, I can't help but praise our Lord. Each of us has been given such wonderful systems that allow us to fulfill His will for our lives. We have much to be thankful for. Thank you for continuing this blog.

Great post, CH. You have quite successfully described the non-falsifiable nature of evolutionary claims. Not holding my breath for any intelligent counter-arguments.

It's basically at the point now where Evo's are throwing up their hands saying "Okay, we don't care how crazy it sounds anymore with all the contradictory data, evolution still dunnit somehow... rapid.. de novo... yea, that's the ticket... no more questions!"

I would love to see you do an article on Orphan Genes, another case of ridiculous de novo storytelling.